Sometime ago, I used carbon copy as I was replacing my hard drive in my Mac Mini running Snow Leopard. Afterwards, on my new drive I had some permission problems.

I've tried several times running a repair permissions / repair disk from disk util. It shows that there are problems and I think it says its correceted the problems.

However the problems remain, what can I do to fix them ?

It doesn't seem to cause me any problems, that I can tell

EDIT

Repairing permissions for “Macintosh HD”
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Italian.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Italian.lproj/UIAgent.nib".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Classes/jconsole.jar".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Home/lib".
User differs on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries", should be 95, user is 0.
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Libraries".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Home/lib/security/cacerts", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Home/lib/security/cacerts".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/Contents/Resources/Java/libdeploy.jnilib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreenLeopard386.app/Contents/Resources/Italian.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreenLeopard386.app/Contents/Resources/Italian.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_CN.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_CN.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/zh_CN.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/zh_CN.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/ko.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/ko.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/ko.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/ko.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/ko.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/ko.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Dutch.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Dutch.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Dutch.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Dutch.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Dutch.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Dutch.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Italian.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Italian.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Italian.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Italian.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Spanish.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Spanish.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Spanish.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Spanish.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Spanish.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Spanish.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/French.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/French.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/French.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/French.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/French.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/French.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/German.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/German.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/German.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/German.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/German.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/German.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Japanese.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Japanese.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Japanese.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/Japanese.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Japanese.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/Japanese.lproj/MainMenu.nib".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/English.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/English.lproj/RemoteDesktopMenu.nib".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired.
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/English.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Remote Desktop Message.app/Contents/Resources/English.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/English.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Support/LockScreen.app/Contents/Resources/English.lproj/MainMenu.nib".
Group differs on "private/var/log/kernel.log", should be 80, group is 0.
Permissions differ on "private/var/log/kernel.log", should be -rw-r----- , they are -rw-r--r-- .
Repaired "private/var/log/kernel.log".
Group differs on "private/var/log/secure.log", should be 80, group is 0.
Permissions differ on "private/var/log/secure.log", should be -rw-r----- , they are -rw-r--r-- .
Repaired "private/var/log/secure.log".
Group differs on "private/var/log/system.log", should be 80, group is 0.
Permissions differ on "private/var/log/system.log", should be -rw-r----- , they are -rw-r--r-- .
Repaired "private/var/log/system.log".

Permissions repair complete